The molecular mechanism underlying the transfer of ubiquitin (Ub) to a substrate consists of three key enzymatic steps. First, ubiquitin itself is adenylated at its C-terminal glycine residue by an activating enzyme (E1). Second, the adenylated Ub forms a covalent linkage to a conjugating enzyme (E2). Finally, a ligating enzyme (E3) recruits both the Ub-charged E2 species and the target protein. There are three classes of E3 enzymes- HECT, RING, and U-box, which are distinguished on the basis of their E2-recruiting domains.

The U-box and RING classes of E3 ligases act as scaffolding molecules that recruit and colocalize both a Ub-charged E2 and the substrate concomitantly. The recruitement of substrate in these proteins involves protein interaction modules such as a WD-40 repeat, TPR, and armadillo repeat domains. In addition to a common organisation, the architecture of U-box and RING domains are similar. Both contain a central alpha-helix flanked by two surface-exposed loops arranged in a cross-brace formation. the structure of RING domains is built around two zinc binding sites that are critical to its stability. In contrast, U-boxes do not bind zinc but have evolved instead networks of hydrogen bonds and salt bridges in corresponding location in the structure. Other similarities between these two domains include an antiparallel beta-sheet type arrangement involving the first surface exposed loop and the central alpha helix. The beta-sheet is stabilised by highly conserved hydrophobic residues responsible for the core packing and stability of the molecule. Most U-box and RING domain structures also contain an elongated C-terminal helix. The physical basis and physiological rationale for evolving distinct U-box and RING E3 ligases are not yet known [(PUBMED:20017557), (PUBMED:11435423), (PUBMED:18393940)].

The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha-fold typical of U-box and RING domains (see PDB:2QIZ). The central alpha helix is flanked by two prominent surface-exposed loop regions. The characteristic network of hydrogen bonds within each loop stabilises the overall structure. The U-box protein appear to catalyze their own ubiquitination as well as that of heterologous substrate [(PUBMED:20017557), (PUBMED:11435423), (PUBMED:18393940)].

The WWE domain: a common interaction module in protein ubiquitination andADP ribosylation.

Trends Biochem Sci. 2001; 26: 273-5

Display abstract

Sequence profile analysis was used to detect a conserved globular domainin several proteins including deltex, Trip12 and poly-ADP-ribosepolymerase homologs. It was named the WWE domain after its most conservedresidues and is predicted to mediate specific protein-protein interactionsin ubiquitin and ADP-ribose conjugation systems.

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with Ubox domain which could be assigned to a KEGG orthologous group, and not all proteins containing Ubox domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.